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Translation Function (translation + function)

Distribution by Scientific Domains
Chemistry100%

Selected Abstracts

Phased rotation, conformation and translation function: theory and computer program

JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2006
Frantisek Pavelcik
A new crystallographic function, phased rotation conformation and translation (PRCTF), has been developed. The function is designed for automatic interpretation of electron density utilizing molecular fragments with some conformational freedom. A computer program, NUT, has been written for the calculation of the PRCTF. [source]

Performance of phased rotation, conformation and translation function: accurate protein model building with tripeptidic and tetrapeptidic fragments

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2010
Franti, ek Pavel
The automatic building of protein structures with tripeptidic and tetrapeptidic fragments was investigated. The oligopeptidic conformers were positioned in the electron-density map by a phased rotation, conformation and translation function and refined by a real-space refinement. The number of successfully located fragments lay within the interval 75,95% depending on the resolution and phase quality. The overlaps of partially located fragments were analyzed. The correctly positioned fragments were connected into chains. Chains formed in this way were extended directly into the electron density and a sequence was assigned. In the initial stage of the model building the number of located fragments was between 60% and 95%, but this number could be increased by several cycles of reciprocal-space refinement and automatic model rebuilding. A nearly complete structure can be obtained on the condition that the resolution is reasonable. Computer graphics will only be needed for a final check and small corrections. [source]

Likelihood-enhanced fast translation functions

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2005
Airlie J. McCoy
This paper is a companion to a recent paper on fast rotation functions [Storoni et al. (2004), Acta Cryst. D60, 432,438], which showed how a Taylor-series expansion of the maximum-likelihood rotation function leads to improved likelihood-enhanced fast rotation functions. In a similar manner, it is shown here how linear and quadratic Taylor-series expansions and least-squares approximations of the maximum-likelihood translation function lead to likelihood-enhanced translation functions, which can be calculated by FFT and which are more sensitive to the correct translation than the traditional correlation-coefficient fast translation function. These likelihood-enhanced translation targets for molecular-replacement searches have been implemented in the program Phaser using the Computational Crystallography Toolbox (cctbx). [source]

Cluster analysis for phasing with molecular replacement: a feasibility study

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2009
Andreas Buehler
Molecular replacement can fail to find a solution, namely a unique orientation and position of a search model, even when many search models are tested under various conditions. Simultaneous use of the results of these searches may help in the solution of such difficult structures. A closeness between the peaks of several calculated rotation functions may identify the model orientation. The largest and most compact cluster of such peaks usually corresponds to models which are oriented similarly to the molecule under study. A search for the optimal translation may be more problematic and both individual translation functions and straightforward cluster analysis in the space of geometric parameters such as rotation angles and translation vectors may give no result. An improvement may be obtained by performing cluster analysis of the peaks of several translation functions in phase-set space. In this case, the Fourier maps computed using the observed structure-factor magnitudes and the phases calculated from differently positioned models are compared. Again, as a rule, the largest and the most compact cluster corresponds to the correct solution. The result of the updated procedure is no longer a single search model but an averaged Fourier map. [source]

Building of RNA and DNA double helices into electron density

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2008
Frantisek Pavelcik
A method has been developed that automatically fits double-helical regions into the electron density of nucleic acid structures. Rigid fragments consisting of two Watson,Crick base pairs and three pairs of phosphate groups in the A-type or B-type conformation are positioned into the electron density by phased rotation and translation functions. The position and orientation of the localized double-helical fragments are determined by phased refinement. The method has been tested by building double-helical regions of nine RNA structures of variable crystallographic resolution and polynucleotide length and is available for free use. [source]

Likelihood-enhanced fast translation functions

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2005
Airlie J. McCoy
This paper is a companion to a recent paper on fast rotation functions [Storoni et al. (2004), Acta Cryst. D60, 432,438], which showed how a Taylor-series expansion of the maximum-likelihood rotation function leads to improved likelihood-enhanced fast rotation functions. In a similar manner, it is shown here how linear and quadratic Taylor-series expansions and least-squares approximations of the maximum-likelihood translation function lead to likelihood-enhanced translation functions, which can be calculated by FFT and which are more sensitive to the correct translation than the traditional correlation-coefficient fast translation function. These likelihood-enhanced translation targets for molecular-replacement searches have been implemented in the program Phaser using the Computational Crystallography Toolbox (cctbx). [source]